Well, this post has nothing to do with java, but I though it would be important, since this issue caused me a lot of frustration. I recently bought a laptop with Windows Vista Home Premium, and I was frustrated at what seemed to me that it was a hardware problem. Well, it wasn't. It was a windows "feature" ;-)
The "feature" that annoyed me was that the screen blinked a couple of times when I was logging in, in a matter that seemed as if the screen is faulty. The same thing happened when I wanted to do something that windows think that I shouldn't do, like moving a read only file, or run an executable program (yet another windows "feature"). When I tried to do any of those actions that would cause a security problem, I got a prompt to ask me if I allow this action, with the desktop disabled, and with an occasional screen blink (totally random).
Well, after some googling, I found the causes of those two really annoying "features". The first "feature" was the Transient Multimon Manager (TMM). This TMM is "a Microsoft Windows Vista operating system feature" responsible for detecting your monitors as you connect/disconnect them to/from your mobile PC. You may regard TMM as a good feature in case you use multiple displays (external monitor, projector, etc.) especially that "TMM persists the user's settings on a per-display basis when possible".
When you seldom use multiple displays (like me), TMM is of no value. So, how do we turn it off? Simple. Go to task scheduler (present under "Accessories/System Tools"), then go to "Task Scheduler Library/Microsoft/Windows/MobilePC", and you'll find a TMM task. Disable it, and you're done (of course you'll have to restart your system for the change to take effect, because the task will already be running). You can also disable the trigger of the task. I do not recommend deleting the task altogether, since you might need it in the future.
Now for the second "feature". Windows vista has what's called "secure desktop". Well, it is a good feature to be frank. When you try to do an action that Vista thinks that it might be the result of a malicious action, it will prompt you whether you allow this action or not. This is not "secure desktop" by the way. Secure desktop is responsible for locking all the processes running in the background so that if the action was really performed by a piece of malicious software, it wouldn't give this piece of software the ability to mimic the user allowing the action to be performed.
So, if you think that you will never have malicious software, and you don't want secure desktop, all you have to do is to run your registry editor (just type "regedit" in the "run" screen), and go to "HKEY_LOCAL_MACHINE/SOFTWARE/Microsoft/Windows/
CurrentVersion/Policies/System", and change the value of the "PromptOnSecureDesktop" to "0" (that's a zero not an O) instead of "1". This will remove secure desktop (hence the occasional blinking) but will not remove the prompting. I recommend that you keep secure desktop for the security reasons, but that's just me.
Edit on 6/1/2008:
I would like to thank Matt for supplying this link in his comment. I think that the screen shot woul give you a little help. Thanks Matt